Import error ("cannot import name Seq") in biopython for both Python 2.7 and 3.6

Question

This is my code:

from Bio.Seq import Seq

from Bio.Alphabet import IUPAC

my_seq = Seq("GATCG", IUPAC.unambiguous_dna)

for index, letter in enumerate(my_seq):

   print("%i %s" %(index, letter))

   print (len(my_seq))

I get an error "Unable to import Seq from Bio.Seq".

Error on terminal is given below:

 Traceback (most recent call last):
  File "sequence-length.py", line 1, in <module>
    from Bio.Seq import Seq
  File "/home/tanuj/.local/lib/python2.7/site-packages/Bio/Seq.py", line 21, in <module>
    import string  # for maketrans only
  File "/home/tanuj/Desktop/biopython/scripts-test/string.py", line 1, in <module>
    from Bio.Seq import Seq
ImportError: cannot import name Seq

I am not sure what the problem is, because the code was working fine, but after some time, the interpreter was unable to import Seq and started showing the error. How can I fix this?

I'll give you a couple of tips before your question gets downvoted. First fix the formatting, your error is unreadable. Second, take your time to elaborate a question and describe it the best possible way, as I don't understand what your problem is and others won't either. Third, explain what have you tried when it was working, and what changed now that it's not working. Cheers ~ — Christopher Francisco, May 09 '18 at 16:07

score 0 · Answer 1 · answered May 09 '18 at 18:30

Your script:

from Bio.Seq import Seq

from Bio.Alphabet import IUPAC

my_seq = Seq("GATCG", IUPAC.unambiguous_dna)

print(len(my_seq))

for index, letter in enumerate(my_seq):

    print(index, letter)

works fine for me in Python 3:

% python3 test.py
5
0 G
1 A
2 T
3 C
4 G

Reading your error messages, my guess your problem is you have a personal code file named string.py ("/home/tanuj/Desktop/biopython/scripts-test/string.py") which Python is confusing with the library string.py it wants to import:

% touch string.py
% python3 test.py
Traceback (most recent call last):
  File "test.py", line 1, in <module>
    from Bio.Seq import Seq
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/Bio/Seq.py", line 25, in <module>
    from Bio._py3k import range
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/Bio/_py3k/__init__.py", line 170, in <module>
    from urllib.request import urlopen, Request, urlretrieve, urlparse, urlcleanup
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 88, in <module>
    import http.client
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 71, in <module>
    import email.parser
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/email/parser.py", line 12, in <module>
    from email.feedparser import FeedParser, BytesFeedParser
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/email/feedparser.py", line 27, in <module>
    from email._policybase import compat32
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/email/_policybase.py", line 7, in <module>
    from email import header
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/email/header.py", line 16, in <module>
    import email.quoprimime
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/email/quoprimime.py", line 44, in <module>
    from string import ascii_letters, digits, hexdigits
ImportError: cannot import name 'ascii_letters'
%

Rename your personal string.py file to something else.

Import error ("cannot import name Seq") in biopython for both Python 2.7 and 3.6

1 Answers1